| | Articles Nucleic Acids Res. 2005 January 1; 33(Database Issue): D1. Published online 2004 December 17. doi: 10.1093/nar/gki133.PMCID: PMC540087 Editorial Dov Greenbaum, Andrew Smith, and Mark Gerstein PMCID: PMC540088 The Molecular Biology Database Collection: 2005 update Michael Y. Galperin PMCID: PMC540093 DDBJ in collaboration with mass-sequencing teams on annotation Y. Tateno, N. Saitou, K. Okubo, H. Sugawara, and T. Gojobori PMCID: PMC539974 The EMBL Nucleotide Sequence Database Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler PMCID: PMC540052 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler PMCID: PMC540017 Database resources of the National Center for Biotechnology Information David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Joan U. Pontius, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O. Suzek, Roman Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko PMCID: PMC540016 The European Bioinformatics Institute's data resources: towards systems biology Catherine Brooksbank, Graham Cameron, and Janet Thornton PMCID: PMC539980 Entrez Gene: gene-centered information at NCBI Donna Maglott, Jim Ostell, Kim D. Pruitt, and Tatiana Tatusova PMCID: PMC539985 HOPPSIGEN: a database of human and mouse processed pseudogenes Khelifi Adel, Duret Laurent, and Mouchiroud Dominique PMCID: PMC540038 NPRD: Nucleosome Positioning Region Database Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, and Nikolay A. Kolchanov PMCID: PMC540003 The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes Y. Lee, J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung, and J. Quackenbush PMCID: PMC540018 ECgene: genome annotation for alternative splicing Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, and Sanghyuk Lee PMCID: PMC540072 SpliceInfo: an information repository for mRNA alternative splicing in human genome Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, and Chen-Chia Huang PMCID: PMC540083 DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants Endre Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, and László Patthy PMCID: PMC540051 The MAPPER database: a multi-genome catalog of putative transcription factor binding sites Voichita D. Marinescu, Isaac S. Kohane, and Alberto Riva PMCID: PMC540057 TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes Abel D. González, Vladimir Espinosa, Ana T. Vasconcelos, Ernesto Pérez-Rueda, and Julio Collado-Vides PMCID: PMC540008 TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies Fang Zhao, Zhenyu Xuan, Lihua Liu, and Michael Q. Zhang PMCID: PMC539958 HuSiDa—the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells Matthias Truss, Maciej Swat, Szymon M. Kielbasa, Reinhold Schäfer, Hanspeter Herzel, and Christian Hagemeier PMCID: PMC540085 NONCODE: an integrated knowledge database of non-coding RNAs Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, and Runsheng Chen PMCID: PMC539995 PolyA_DB: a database for mammalian mRNA polyadenylation Haibo Zhang, Jun Hu, Michael Recce, and Bin Tian PMCID: PMC540009 Rfam: annotating non-coding RNAs in complete genomes Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, and Alex Bateman PMCID: PMC540035 RNAdb—a comprehensive mammalian noncoding RNA database Ken C. Pang, Stuart Stephen, Pär G. Engström, Khairina Tajul-Arifin, Weisan Chen, Claes Wahlestedt, Boris Lenhard, Yoshihide Hayashizaki, and John S. Mattick PMCID: PMC540043 siRNAdb: a database of siRNA sequences Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, and Erik L. L. Sonnhammer PMCID: PMC540090 The Small Subunit rRNA Modification Database James A. McCloskey and Jef Rozenski PMCID: PMC539969 Compilation of tRNA sequences and sequences of tRNA genes Mathias Sprinzl and Konstantin S. Vassilenko PMCID: PMC539966 UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul J. Kersey, Jorge Duarte, Cecilia Saccone, and Graziano Pesole PMCID: PMC539975 PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, and Nicholas Lamb PMCID: PMC540074 The Universal Protein Resource (UniProt) Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, and Lai-Su L. Yeh PMCID: PMC540024 NMPdb: Database of Nuclear Matrix Proteins Sven Mika and Burkhard Rost PMCID: PMC540086 PSORTdb: a protein subcellular localization database for bacteria Sébastien Rey, Michael Acab, Jennifer L. Gardy, Matthew R. Laird, Katalin deFays, Christophe Lambert, and Fiona S. L. Brinkman PMCID: PMC539981 SPD—a web-based secreted protein database Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, and Jingchu Luo PMCID: PMC540047 TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations Ya-Hui Chang, Wen-Hui Su, Tso-Ching Lee, Hsiao-Fang Sunny Sun, Chia-Hsiang Chen, Wen-Harn Pan, Shih-Feng Tsai, and Yuh-Shan Jou PMCID: PMC540056 eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity Qiaojuan Jane Su, Lin Lu, Serge Saxonov, and Douglas L. Brutlag PMCID: PMC540014 PDBSite: a database of the 3D structure of protein functional sites Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, and Nickolay A. Kolchanov PMCID: PMC540059 ADDA: a domain database with global coverage of the protein universe Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, and Liisa Holm PMCID: PMC540050 CDD: a Conserved Domain Database for protein classification Aron Marchler-Bauer, John B. Anderson, Praveen F. Cherukuri, Carol DeWeese-Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, and Stephen H. Bryant PMCID: PMC540023 FunShift: a database of function shift analysis on protein subfamilies Saraswathi Abhiman and Erik L. L. Sonnhammer PMCID: PMC540021 InterPro, progress and status in 2005 Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell, Anastasia N. Nikolskaya, Sandra Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, and Cathy H. Wu PMCID: PMC540060 PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes Shu-Hsien Sheu, David R. Lancia, Jr, Karl H. Clodfelter, Melissa R. Landon, and Sandor Vajda PMCID: PMC540045 The ProDom database of protein domain families: more emphasis on 3D Catherine Bru, Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar, and Daniel Kahn PMCID: PMC539988 ProtoNet 4.0: A hierarchical classification of one million protein sequences Noam Kaplan, Ori Sasson, Uri Inbar, Moriah Friedlich, Menachem Fromer, Hillel Fleischer, Elon Portugaly, Nathan Linial, and Michal Linial PMCID: PMC539961 S4: structure-based sequence alignments of SCOP superfamilies James Casbon and Mansoor A. S. Saqi PMCID: PMC539997 The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines Kristian Vlahoviček, László Kaján, Vilmos Ágoston, and Sándor Pongor PMCID: PMC540066 The SYSTERS Protein Family Database in 2005 Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, and Eike Staub PMCID: PMC539984 REBASE—restriction enzymes and DNA methyltransferases Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis PMCID: PMC539983 The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema Nita Deshpande, Kenneth J. Addess, Wolfgang F. Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John Westbrook, Helen M. Berman, and Philip E. Bourne PMCID: PMC540011 PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures Jae-Min Shin and Doo-Ho Cho PMCID: PMC540013 Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB Thomas Lütteke, Martin Frank, and Claus-W. von der Lieth PMCID: PMC539967 The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis Frances Pearl, Annabel Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony Lewis, Christopher Bennett, Russell Marsden, Alistair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew Harrison, Timothy Dallman, Gabrielle Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio Sillero, Janet Thornton, and Christine Orengo PMCID: PMC539978 GenDiS: Genomic Distribution of protein structural domain Superfamilies Ganesan Pugalenthi, Anirban Bhaduri, and Ramanathan Sowdhamini PMCID: PMC540041 IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes Véronique Giudicelli, Denys Chaume, and Marie-Paule Lefranc PMCID: PMC539964 E-MSD: an integrated data resource for bioinformatics S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, D. Barrell, R. Apweiler, and K. Henrick PMCID: PMC540012 PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids Roman A. Laskowski, Victor V. Chistyakov, and Janet M. Thornton PMCID: PMC539955 STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database Goran Neshich, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Ivan P. Pinto, Juliana F. Palandrani, João N. Krauchenco, Christian Baudet, Arnaldo J. Montagner, and Roberto H. Higa PMCID: PMC540065 PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank Gábor E. Tusnády, Zsuzsanna Dosztányi, and István Simon PMCID: PMC539956 PFD: a database for the investigation of protein folding kinetics and stability Kate F. Fulton, Glyn L. Devlin, Rachel A. Jodun, Linda Silvestri, Stephen P. Bottomley, Alan R. Fersht, and Ashley M. Buckle PMCID: PMC539970 The PANTHER database of protein families, subfamilies, functions and pathways Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano, and Paul D. Thomas PMCID: PMC540032 Biomedical term mapping databases Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, and Russ B. Altman PMCID: PMC540091 The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis J. R. Cole, B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje PMCID: PMC539992 Integr8 and Genome Reviews: integrated views of complete genomes and proteomes Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter Mclaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, and Rolf Apweiler PMCID: PMC539993 PartiGeneDB—collating partial genomes José M. Peregrín-Alvarez, Andrew Yam, Gaya Sivakumar, and John Parkinson PMCID: PMC540063 The PEDANT genome database in 2005 M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, and Dmitrij Frishman PMCID: PMC539973 Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource Elliot J. Lefkowitz, Chris Upton, Shankar S. Changayil, Charles Buck, Paula Traktman, and R. Mark L. Buller PMCID: PMC540064 BacMap: an interactive picture atlas of annotated bacterial genomes Paul Stothard, Gary Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph Cruz, Michael Ellison, and David S. Wishart PMCID: PMC540029 Metagrowth: a new resource for the building of metabolic hypotheses in microbiology Hiroyuki Ogata and Jean-Michel Claverie PMCID: PMC539996 VFDB: a reference database for bacterial virulence factors Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, and Qi Jin PMCID: PMC539962 EchoBASE: an integrated post-genomic database for Escherichia coli Raju V. Misra, Richard S. P. Horler, Wolfgang Reindl, Igor I. Goryanin, and Gavin H. Thomas PMCID: PMC539982 EcoCyc: a comprehensive database resource for Escherichia coli Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne Paley, Ian T. Paulsen, Martín Peralta-Gil, and Peter D. Karp PMCID: PMC540062 Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation Geoffrey L. Winsor, Raymond Lo, Shannan J. Ho Sui, Korine S.E. Ung, Shaoshan Huang, Dean Cheng, Wai-Kay Ho Ching, Robert E. W. Hancock, and Fiona S. L. Brinkman PMCID: PMC540001 The Diatom EST Database Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, and Chris Bowler PMCID: PMC540075 The Ashbya Genome Database (AGD)—a tool for the yeast community and genome biologists Leandro Hermida, Sophie Brachat, Sylvia Voegeli, Peter Philippsen, and Michael Primig PMCID: PMC539963 CandidaDB: a genome database for Candida albicans pathogenomics C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, F. Tekaia, O. Bader, Antje Albrecht, L. Castillo, A. Dominguez, J. F. Ernst, C. Fradin, C. Gaillardin, S. Garcia-Sanchez, P. de Groot, B. Hube, F. M. Klis, S. Krishnamurthy, D. Kunze, M.-C. Lopez, A. Mavor, N. Martin, I. Moszer, D. Onésime, J. Perez Martin, R. Sentandreu, E. Valentin, and A. J. P. Brown PMCID: PMC540078 The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Gail Binkley, Christopher Lane, Stuart R. Miyasato, and Gavin Sherlock PMCID: PMC539957 CYGD: the Comprehensive Yeast Genome Database U. Güldener, M. Münsterkötter, G. Kastenmüller, N. Strack, J. van Helden, C. Lemer, J. Richelles, S. J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, H. Michael, A. Kaps, E. Talla, B. Dujon, B. André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, and H. W. Mewes PMCID: PMC540007 PROPHECY—a database for high-resolution phenomics Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Ilona Pylvänäinen, Graham J. L. Kemp, Olle Nerman, and Anders Blomberg PMCID: PMC540080 Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD) Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert Nash, Rose Oughtred, Marek Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, and J. Michael Cherry PMCID: PMC539977 The Yeast Resource Center Public Data Repository Michael Riffle, Lars Malmström, and Trisha N. Davis PMCID: PMC540027 WormBase: a comprehensive data resource for Caenorhabditis biology and genomics Nansheng Chen, Todd W. Harris, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Payan Canaran, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Fiona Cunningham, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Shraddha Pai, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, and Lincoln D. Stein PMCID: PMC540020 FlyBase: genes and gene models Rachel A. Drysdale and Madeline A. Crosby PMCID: PMC540000 MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates Andre R. O. Cavalcanti, Thomas H. Clarke, and Laura F. Landweber PMCID: PMC540084 SilkDB: a knowledgebase for silkworm biology and genomics Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, and Jun Yu PMCID: PMC540070 SilkSatDb: a microsatellite database of the silkworm, Bombyx mori M. D. Prasad, M. Muthulakshmi, K. P. Arunkumar, M. Madhu, V. B. Sreenu, V. Pavithra, B. Bose, H. A. Nagarajaram, K. Mita, T. Shimada, and J. Nagaraju PMCID: PMC540053 EzCatDB: the Enzyme Catalytic-mechanism Database Nozomi Nagano PMCID: PMC540034 3did: interacting protein domains of known three-dimensional structure Amelie Stein, Robert B. Russell, and Patrick Aloy PMCID: PMC539991 The Biomolecular Interaction Network Database and related tools 2005 update C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, D. Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, I. Donaldson, D. Dorairajoo, M. J. Dumontier, M. R. Dumontier, V. Earles, R. Farrall, H. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, R. Haw, A. Hrvojic, L. Hurrell, R. Isserlin, F. Jack, F. Juma, A. Khan, T. Kon, S. Konopinsky, V. Le, E. Lee, S. Ling, M. Magidin, J. Moniakis, J. Montojo, S. Moore, B. Muskat, I. Ng, J. P. Paraiso, B. Parker, G. Pintilie, R. Pirone, J. J. Salama, S. Sgro, T. Shan, Y. Shu, J. Siew, D. Skinner, K. Snyder, R. Stasiuk, D. Strumpf, B. Tuekam, S. Tao, Z. Wang, M. White, R. Willis, C. Wolting, S. Wong, A. Wrong, C. Xin, R. Yao, B. Yates, S. Zhang, K. Zheng, T. Pawson, B. F. F. Ouellette, and C. W. V. Hogue PMCID: PMC540005 GeneNet in 2005 E. A. Ananko, N. L. Podkolodny, I. L. Stepanenko, O. A. Podkolodnaya, D. A. Rasskazov, D. S. Miginsky, V. A. Likhoshvai, A. V. Ratushny, N. N. Podkolodnaya, and N. A. Kolchanov PMCID: PMC540031 Reactome: a knowledgebase of biological pathways G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, B. Jassal, G.R. Gopinath, G.R. Wu, L. Matthews, S. Lewis, E. Birney, and L. Stein PMCID: PMC540026 STRING: known and predicted protein–protein associations, integrated and transferred across organisms Christian von Mering, Lars J. Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, and Peer Bork PMCID: PMC539959 ChickVD: a sequence variation database for the chicken genome Jing Wang, Ximiao He, Jue Ruan, Mingtao Dai, Jie Chen, Yong Zhang, Yafeng Hu, Chen Ye, Shengting Li, Lijuan Cong, Lin Fang, Bin Liu, Songgang Li, Jian Wang, David W. Burt, Gane Ka-Shu Wong, Jun Yu, Huanming Yang, and Jun Wang PMCID: PMC540046 DED: Database of Evolutionary Distances Vamsi Veeramachaneni and Wojciech Makałowski PMCID: PMC540048 Ensembl 2005 T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and E. Birney PMCID: PMC540092 The UCSC Proteome Browser Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, and W. James Kent PMCID: PMC540054 The Vertebrate Genome Annotation (Vega) database J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, L. Wilming, and T. Hubbard PMCID: PMC540089 Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew Weirauch, Richard Burhans, Webb Miller, and Ross C. Hardison PMCID: PMC539999 The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, and Judith A. Blake PMCID: PMC540067 Inparanoid: a comprehensive database of eukaryotic orthologs Kevin P. O'Brien, Maido Remm, and Erik L. L. Sonnhammer PMCID: PMC540061 Polymorphix: a sequence polymorphism database Eric Bazin, Laurent Duret, Simon Penel, and Nicolas Galtier PMCID: PMC540030 The Rat Genome Database (RGD): developments towards a phenome database Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R. Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne Kwitek, Peter Tonellato, and Howard Jacob PMCID: PMC540004 RatMap—rat genome tools and data Greta Petersen, Per Johnson, Lars Andersson, Karin Klinga-Levan, Pedro M. Gómez-Fabre, and Fredrik Ståhl PMCID: PMC540079 The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sælensminde, and David A. Liberles PMCID: PMC540044 L1Base: from functional annotation to prediction of active LINE-1 elements Tobias Penzkofer, Thomas Dandekar, and Tomasz Zemojtel PMCID: PMC539998 NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott PMCID: PMC539979 DG-CST (Disease Gene Conserved Sequence Tags), a database of human–mouse conserved elements associated to disease genes Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, and Sandro Banfi PMCID: PMC539965 HCAD, closing the gap between breakpoints and genes Robert Hoffmann, Joaquin Dopazo, Juan C. Cigudosa, and Alfonso Valencia PMCID: PMC540015 Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders Ada Hamosh, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, and Victor A. McKusick PMCID: PMC539987 FESD: a Functional Element SNPs Database in human Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, and Young Joo Kim PMCID: PMC540036 IPD—the Immuno Polymorphism Database James Robinson, Matthew J. Waller, Peter Stoehr, and Steven G. E. Marsh PMCID: PMC539986 SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs Joke Reumers, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, and Frederic Rousseau PMCID: PMC540040 Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, and Kenta Nakai PMCID: PMC540071 HAGR: the Human Ageing Genomic Resources João Pedro de Magalhães, Joana Costa, and Olivier Toussaint PMCID: PMC539971 T1DBase, a community web-based resource for type 1 diabetes research Luc J. Smink, Erin M. Helton, Barry C. Healy, Christopher C. Cavnor, Alex C. Lam, Daisy Flamez, Oliver S. Burren, Yang Wang, Geoffrey E. Dolman, David B. Burdick, Vincent H. Everett, Gustavo Glusman, Davide Laneri, Lee Rowen, Helen Schuilenburg, Neil M. Walker, Josyf Mychaleckyj, Linda S. Wicker, Decio L. Eizirik, John A. Todd, and Nathan Goodman PMCID: PMC540049 5′SAGE: 5′-end Serial Analysis of Gene Expression database Yasuhiro Kasai, Shin-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, and Shinichi Morishita PMCID: PMC540039 ArrayExpress—a public repository for microarray gene expression data at the EBI H. Parkinson, U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. Garcia Lara, E. Holloway, M. Kapushesky, P. Lilja, G. Mukherjee, A. Oezcimen, T. Rayner, P. Rocca-Serra, A. Sharma, S. Sansone, and A. Brazma PMCID: PMC540010 GeneTide—Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases Maxim Shklar, Liora Strichman-Almashanu, Orit Shmueli, Michael Shmoish, Marilyn Safran, and Doron Lancet PMCID: PMC540076 NCBI GEO: mining millions of expression profiles—database and tools Tanya Barrett, Tugba O. Suzek, Dennis B. Troup, Stephen E. Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex E. Lash, Wataru Fujibuchi, and Ron Edgar PMCID: PMC539976 The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms Motohiko Tanino, Marie-Anne Debily, Takuro Tamura, Teruyoshi Hishiki, Osamu Ogasawara, Katsuji Murakawa, Shoko Kawamoto, Kouichi Itoh, Shinya Watanabe, Sandro José de Souza, Sandrine Imbeaud, Esther Graudens, Eric Eveno, Phillip Hilton, Yukio Sudo, Janet Kelso, Kazuho Ikeo, Tadashi Imanishi, Takashi Gojobori, Charles Auffray, Winston Hide, and Kousaku Okubo PMCID: PMC540058 SIEGE: Smoking Induced Epithelial Gene Expression Database Vishal Shah, Sriram Sridhar, Jennifer Beane, Jerome S. Brody, and Avrum Spira PMCID: PMC539989 The Stanford Microarray Database accommodates additional microarray platforms and data formats Catherine A. Ball, Ihab A. B. Awad, Janos Demeter, Jeremy Gollub, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, and Gavin Sherlock PMCID: PMC539960 DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels Oliver Drews and Angelika Görg PMCID: PMC540055 MetaRouter: bioinformatics for bioremediation Florencio Pazos, David Guijas, Alfonso Valencia, and Victor De Lorenzo PMCID: PMC540022 IMGT, the international ImMunoGeneTics information system® Marie-Paule Lefranc, Véronique Giudicelli, Quentin Kaas, Elodie Duprat, Joumana Jabado-Michaloud, Dominique Scaviner, Chantal Ginestoux, Oliver Clément, Denys Chaume, and Gérard Lefranc PMCID: PMC540019 Organelle DB: a cross-species database of protein localization and function Nuwee Wiwatwattana and Anuj Kumar PMCID: PMC540025 AMPDB: the Arabidopsis Mitochondrial Protein Database Joshua L. Heazlewood and A. Harvey Millar PMCID: PMC540002 MITOMAP: a human mitochondrial genome database—2004 update Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, and Douglas C. Wallace PMCID: PMC540033 BarleyBase—an expression profiling database for plant genomics Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, and Julie A. Dickerson PMCID: PMC540077 CR-EST: a resource for crop ESTs C. Künne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, and U. Scholz PMCID: PMC540073 openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections Stephen Rudd PMCID: PMC539994 PlantMarkers—a database of predicted molecular markers from plants Stephen Rudd, Heiko Schoof, and Klaus Mayer PMCID: PMC540028 Arabidopsis nucleolar protein database (AtNoPDB) John W. S. Brown, Peter J. Shaw, Paul Shaw, and David F. Marshall PMCID: PMC540006 ASRP: the Arabidopsis Small RNA Project Database Adam M. Gustafson, Edwards Allen, Scott Givan, Daniel Smith, James C. Carrington, and Kristin D. Kasschau PMCID: PMC540081 GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts Sébastien Aubourg, Véronique Brunaud, Clémence Bruyère, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, Patrice Déhais, Gilbert Deléage, Aymeric Duclert, Manuel Echeverria, Aimée Eschbach, Denis Falconet, Ghislain Filippi, Christine Gaspin, Christophe Geourjon, Jean-Michel Grienenberger, Guy Houlné, Elisabeth Jamet, Frédéric Lechauve, Olivier Leleu, Philippe Leroy, Régis Mache, Christian Meyer, Hafed Nedjari, Ioan Negrutiu, Valérie Orsini, Eric Peyretaillade, Cyril Pommier, Jeroen Raes, Jean-Loup Risler, Stéphane Rivière, Stéphane Rombauts, Pierre Rouzé, Michel Schneider, Philippe Schwob, Ian Small, Ghislain Soumayet-Kampetenga, Darko Stankovski, Claire Toffano, Michael Tognolli, Michel Caboche, and Alain Lecharny PMCID: PMC540069 RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, and Kazuo Shinozaki PMCID: PMC539968 Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics Yuichi Ito, Kohji Arikawa, Baltazar A. Antonio, Isamu Ohta, Shinji Naito, Yoshiyuki Mukai, Atsuko Shimano, Masatoshi Masukawa, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Junri Yokoyama, Yasumichi Sakai, Katsumi Sakata, Yoshiaki Nagamura, Nobukazu Namiki, Takashi Matsumoto, Kenichi Higo, and Takuji Sasaki PMCID: PMC540037 Brassica ASTRA: an integrated database for Brassica genomic research Christopher G. Love, Andrew J. Robinson, Geraldine A. C. Lim, Clare J. Hopkins, Jacqueline Batley, Gary Barker, German C. Spangenberg, and David Edwards PMCID: PMC539990 The Legume Information System (LIS): an integrated information resource for comparative legume biology Michael D. Gonzales, Eric Archuleta, Andrew Farmer, Kamal Gajendran, David Grant, Randy Shoemaker, William D. Beavis, and Mark E. Waugh PMCID: PMC540082 PoMaMo—a comprehensive database for potato genome data Svenja Meyer, Axel Nagel, and Christiane Gebhardt PMCID: PMC539972 VBASE2, an integrative V gene database Ida Retter, Hans Helmar Althaus, Richard Münch, and Werner Müller PMCID: PMC540042 Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences Susie M. Stephens, Jake Y. Chen, Marcel G. Davidson, Shiby Thomas, and Barry M. Trute PMCID: PMC540068 |
